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- PDB-5y84: Hapalindole U and DMSPP Bound AmbP3 -

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Basic information

Entry
Database: PDB / ID: 5y84
TitleHapalindole U and DMSPP Bound AmbP3
ComponentsAmbP3
KeywordsTRANSFERASE / Prenyltransferase
Function / homologyhapalindole G dimethylallyltransferase / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / Hapalindole U / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Hapalindole dimethylallyltransferase
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWong, C.P. / Awakawa, T. / Nakashima, Y.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3
Authors: Wong, C.P. / Awakawa, T. / Nakashima, Y. / Mori, T. / Zhu, Q. / Liu, X. / Abe, I.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmbP3
B: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2216
Polymers76,0882
Non-polymers1,1334
Water5,188288
1
A: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6113
Polymers38,0441
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-3 kcal/mol
Surface area11600 Å2
MethodPISA
2
B: AmbP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6113
Polymers38,0441
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-2 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.311, 54.810, 77.087
Angle α, β, γ (deg.)105.42, 106.24, 98.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AmbP3


Mass: 38044.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Gene: ambP3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V5TDY7
#2: Chemical ChemComp-8P6 / Hapalindole U


Mass: 304.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N2
#3: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG 8000, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1.1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→29.6 Å / Num. obs: 44715 / % possible obs: 97.4 % / Redundancy: 3.3 % / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.465 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata processing
Aimlessdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4G

5y4g


Resolution: 2→26.428 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.02
RfactorNum. reflection% reflection
Rfree0.2585 1990 4.45 %
Rwork0.2115 --
obs0.2136 44715 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→26.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 74 288 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074818
X-RAY DIFFRACTIONf_angle_d0.8946602
X-RAY DIFFRACTIONf_dihedral_angle_d8.8383781
X-RAY DIFFRACTIONf_chiral_restr0.05724
X-RAY DIFFRACTIONf_plane_restr0.007854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33381400.29563010X-RAY DIFFRACTION97
2.05-2.10540.32581440.26283064X-RAY DIFFRACTION97
2.1054-2.16730.29331350.23872966X-RAY DIFFRACTION96
2.1673-2.23730.30541530.23353065X-RAY DIFFRACTION97
2.2373-2.31720.27971450.23543044X-RAY DIFFRACTION97
2.3172-2.40990.30631440.23173052X-RAY DIFFRACTION97
2.4099-2.51950.31971320.22493060X-RAY DIFFRACTION97
2.5195-2.65220.26711420.23273050X-RAY DIFFRACTION98
2.6522-2.81820.28561450.22223066X-RAY DIFFRACTION98
2.8182-3.03550.28871470.22513080X-RAY DIFFRACTION98
3.0355-3.34040.3021460.21823064X-RAY DIFFRACTION98
3.3404-3.82260.22381310.19153072X-RAY DIFFRACTION98
3.8226-4.81130.19471450.17153081X-RAY DIFFRACTION98
4.8113-26.43080.21911410.19623051X-RAY DIFFRACTION97

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